| Stage | Agent | Special Agent | Perfect Agent |
| dataDyne Central - Defection | 0:06 | 0:48 | 1:53 |
| datadyne Central - Investigation | 1:32 | 2:17 | 2:48 |
| dataDyne Central - Extraction | 0:54 | 1:37 | 1:51 |
| Carrington Villa - Hostage One | 1:12 | 1:25 | 1:41 |
| Chicago - Stealth | 0:16 | 0:30 | 0:34 |
| G5 Building - Reconnaissance | 0:46 | 0:55 | 1:11 |
| Area 51 - Infiltration | 1:18 | 1:47 | 1:55 |
| Area 51 - Rescue | 1:31 | 2:25 | 3:00 |
| Area 51 - Escape | 2:30 | 3:30 | 3:38 |
| Air Base - Espionage | 1:19 | 1:52 | 2:19 |
| Air Force One - Antiterrorism | 0:59 | 1:27 | 1:35 |
| Crash Site - Confrontation | 1:21 | 1:32 | 1:59 |
| Pelagic II - Exploration | 0:56 | 1:57 | 2:21 |
| Deep Sea - Nullify Threat | 2:30 | 2:59 | 3:27 |
| Carrington Institute - Defense | 0:55 | 1:34 | 1:58 |
| Attack Ship - Covert Assault | 2:18 | 2:37 | 3:20 |
| Skedar Ruins - Battle Shrine | 1:15 | 1:33 | 1:46 |
| Mr. Blonde's Revenge | 1:34 | 1:35 | 1:44 |
| Maian SOS | 1:39 | 2:08 | 2:33 |
| WAR! | 0:28 | 0:51 | 1:00 |
| The Duel | 0:03 | 0:06 | 0:09 |
| Total Time | ? | ? | ? |